We have used the free tool Argus Lab for geometry opt of the protein. For small protein it will work, but u can try it. Use UFF & BFGS options. Did u checked the Ramachandran plot of your protein?
Subject: Re: [gmx-users] Re: error during the minimization thanks for your advice Mr. Manoj I tried the same simulation by taking a structure which was already minimized by another software Amber. Using that structure as the starting structure also, i got the same error i mention earlier. please suggest me something thanks -- M.N. MANOJ PROJECT LEADER - BIOINFORMATICS VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION BANGALORE INDIA
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